Allow script-based schema patches that can use API in addition to pure SQL-based patches

modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm

@@ -119,10 +119,12 @@ sub new {
                 || die "DB($safe_url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
                       ."Unfortunately we cannot patch the database; you may have to create a new database or agree to run older code\n";
 
-            my $patcher_command = "$ENV{'EHIVE_ROOT_DIR'}/scripts/db_cmd.pl -url $safe_url";
+            my $sql_patcher_command = "$ENV{'EHIVE_ROOT_DIR'}/scripts/db_cmd.pl -url $safe_url";
 
             die "DB($safe_url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"
-               ."Please upgrade the database by applying the following patches:\n\n".join("\n", map { "\t$patcher_command < $_" } @$new_patches)."\n\nand try again.\n";
+               ."Please upgrade the database by applying the following patches:\n\n"
+               .join("\n", map { ($_=~/\.\w*sql\w*$/) ? "\t$sql_patcher_command < $_" : "$_ -url $safe_url" } @$new_patches)
+               ."\n\nand try again.\n";
 
         } elsif($code_sql_schema_version < $db_sql_schema_version) {
 

modules/Bio/EnsEMBL/Hive/DBSQL/SqlSchemaAdaptor.pm

@@ -42,11 +42,13 @@ sub find_all_sql_schema_patches {
     my %all_patches = ();
 
     if(my $hive_root_dir = $ENV{'EHIVE_ROOT_DIR'} ) {
-        foreach my $patch_path ( split(/\n/, `ls -1 $hive_root_dir/sql/patch_20*.*sql*`) ) {
+        foreach my $patch_path ( split(/\n/, `ls -1 $hive_root_dir/sql/patch_20*.*`) ) {
             my ($patch_name, $driver) = ($patch_path=~/^(.+)\.(\w+)$/);
 
             $driver = 'mysql' if ($driver eq 'sql');    # for backwards compatibility
 
+            $driver = 'script' if ($driver!~/sql/);
+
             $all_patches{$patch_name}{$driver} = $patch_path;
         }
     } # otherwise will sliently return an empty hash
@@ -63,8 +65,10 @@ sub get_sql_schema_patches {
 
     my @ordered_patches = ();
     foreach my $patch_key ( (sort keys %$all_patches)[$after_version..$code_schema_version-1] ) {
-        if(my $patch_path = $all_patches->{$patch_key}{$driver}) {
-            push @ordered_patches, $patch_path;
+        if(my $sql_patch_path = $all_patches->{$patch_key}{$driver}) {
+            push @ordered_patches, $sql_patch_path;
+        } elsif(my $script_patch_path = $all_patches->{$patch_key}{'script'}) {
+            push @ordered_patches, $script_patch_path;
         } else {
             return;
         }